[med-svn] r15368 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-12-01 09:02:32 +0000 (Sun, 01 Dec 2013)
New Revision: 15368

Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
New upstream version


Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2013-12-01 08:45:10 UTC (rev 15367)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2013-12-01 09:02:32 UTC (rev 15368)
@@ -1,3 +1,11 @@
+r-bioc-rsamtools (1.14.2-1) unstable; urgency=low
+
+  * New upstream version (adapted patch)
+    Closes: #730984
+  * Build-Depends: r-bioc-xvector
+
+ -- Andreas Tille <tille at debian.org>  Sun, 01 Dec 2013 09:45:58 +0100
+
 r-bioc-rsamtools (1.12.4-1) unstable; urgency=low
 
   * Initial release (closes: #728285)

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2013-12-01 08:45:10 UTC (rev 15367)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2013-12-01 09:02:32 UTC (rev 15368)
@@ -11,6 +11,7 @@
                r-bioc-iranges,
                r-bioc-biostrings,
                r-bioc-genomicranges,
+               r-bioc-xvector,
                libbam-dev
 Standards-Version: 3.9.4
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
@@ -26,7 +27,8 @@
          r-bioc-biocgenerics,
          r-bioc-iranges,
          r-bioc-biostrings,
-         r-bioc-genomicranges
+         r-bioc-genomicranges,
+         r-bioc-xvector
 # The following BioConductor modules are not yet packaged but used in the unit test
 Suggests: r-bioc-pasillabamsubset, r-bioc-shortread
 Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2013-12-01 08:45:10 UTC (rev 15367)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2013-12-01 09:02:32 UTC (rev 15368)
@@ -1,26 +1,27 @@
 Author: Andreas Tille <tille at debian.org>
-LastChanged: Wed, 04 Sep 2013 11:11:22 +0200
+LastChanged: Sun, 01 Dec 2013 09:45:58 +0100
 Description: If the systems includes zlib natively there is no point in
  requiring the import of zlibbioc
 
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
-@@ -14,7 +14,7 @@ License: Artistic-2.0 + file LICENSE
+@@ -14,7 +14,7 @@ License: Artistic-2.0 | file LICENSE
  LazyLoad: yes
- Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.11.38),
-         Biostrings (>= 2.25.6)
--Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc,
-+Imports: methods, utils, IRanges, GenomicRanges, Biostrings,
-         bitops, BiocGenerics (>= 0.1.3)
- Suggests: ShortRead (>= 1.13.19), GenomicFeatures,
-         TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset,
+ Depends: methods, IRanges (>= 1.19.11), GenomicRanges (>= 1.13.35),
+         XVector, Biostrings (>= 2.29.7)
+-Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops
++Imports: utils, BiocGenerics (>= 0.1.3), bitops
+ Suggests: ShortRead (>= 1.19.10), GenomicFeatures,
+         TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
+         TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
 --- a/NAMESPACE
 +++ b/NAMESPACE
-@@ -1,7 +1,5 @@
- useDynLib(Rsamtools, .registration=TRUE)
+@@ -2,8 +2,6 @@ useDynLib(Rsamtools, .registration=TRUE)
  
+ import(methods)
+ 
 -import(zlibbioc)
 -
+ import(XVector)
+ 
  importFrom(bitops, bitAnd)
- 
- importFrom(utils, read.table)           # normalizePath --> base in R-2.13